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Genes 2019, 10(1), 45; https://doi.org/10.3390/genes10010045

Network Analyses of Integrated Differentially Expressed Genes in Papillary Thyroid Carcinoma to Identify Characteristic Genes

1
School of Statistics, Qufu Normal University, Qufu 273165, China
2
School of Information Science and Engineering, Qufu Normal University, Rizhao 276800, China
3
School of Computer Science and Technology, Xidian University, Xi’an 710071, China
4
College of Life Science, Qufu Normal University, Qufu 273165, China
*
Author to whom correspondence should be addressed.
Received: 8 November 2018 / Revised: 26 December 2018 / Accepted: 9 January 2019 / Published: 14 January 2019
PDF [695 KB, uploaded 14 January 2019]   |   Review Reports

Abstract

Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer. Identifying characteristic genes of PTC are of great importance to reveal its potential genetic mechanisms. In this paper, we proposed a framework, as well as a measure named Normalized Centrality Measure (NCM), to identify characteristic genes of PTC. The framework consisted of four steps. First, both up-regulated genes and down-regulated genes, collectively called differentially expressed genes (DEGs), were screened and integrated together from four datasets, that is, GSE3467, GSE3678, GSE33630, and GSE58545; second, an interaction network of DEGs was constructed, where each node represented a gene and each edge represented an interaction between linking nodes; third, both traditional measures and the NCM measure were used to analyze the topological properties of each node in the network. Compared with traditional measures, more genes related to PTC were identified by the NCM measure; fourth, by mining the high-density subgraphs of this network and performing Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, several meaningful results were captured, most of which were demonstrated to be associated with PTC. The experimental results proved that this network framework and the NCM measure are useful for identifying more characteristic genes of PTC.
Keywords: differentially expressed genes (DEGs); interaction network; papillary thyroid cancer (PTC); Normalized Centrality Measure (NCM) differentially expressed genes (DEGs); interaction network; papillary thyroid cancer (PTC); Normalized Centrality Measure (NCM)
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).
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Shang, J.; Ding, Q.; Yuan, S.; Liu, J.-X.; Li, F.; Zhang, H. Network Analyses of Integrated Differentially Expressed Genes in Papillary Thyroid Carcinoma to Identify Characteristic Genes. Genes 2019, 10, 45.

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